GWAS and QTLanalysis for 124 individual traits

Investigating the genetic architecture of important agronomic traits in grapevine, like grape quality and resilience to abiotic stress, has been hampered by bottlenecks in genotyping and phenotyping. Here, we developed a high-density 200K single nucleotide polymorphism array and validated its effectiveness by genotyping 471 accessions from three F1 breeding populations. We developed a high-throughput grape phenotyping tool that accurately captures berry color, shape and size. By integrating data from the two platforms, associated loci were identified over three growing seasons. Association mapping, and haplotype analysis identified novel loci and candidate genes for berry shape (bHLH017), soluble sugars (ACT) and organic acids (ALTM1 and FUSC2), as well as vine cold tolerance (NAC08), and fine mapped the flower sex determination locus. Furthermore, we validated the functional role of NAC08, demonstrating that it activated the expression of RFS6 to increase raffinose levels and confer cold tolerance. Together, these augmented tools, the integrated data, and novel loci establish a better foundation for trait aggregation that will enhance breeding efficiency and boost the development of high-quality grape varieties.